In the August 2002 edition of the journal Animal Genetics, Dr. Emmeline Hill and her colleagues at the Department of Genetics, Trinity College, Dublin, Ireland, published a ground-breaking study that changes much of what we thought we knew about the early history of the thoroughbred, and that affects the pedigrees of virtually every thoroughbred now living. It is not, as Dr. Hill says, the "definitive" study; still, it is the first to apply the power of mtDNA research to the history of thoroughbred matrilines.

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Dr. Hill generously offered to share her research with us, and Blackwell Publishing has allowed us to post the original Animal Geneticsarticle here, so that our audience can read it in its entirety. Below is an examination of the research, placed in a broader historic context -- Dr. Hill did not review the essay below, and is not responsible for any errors there may be in misinterpretation. A simplified guide to the language of genetics, by geneticist Michael Bowling, can be read here. Mr. Bowling and his wife, Dr. Ann Bowling, co-authored the first studies of the practical application of mtDNA analysis to horses, specifically Arabians. Special thanks to Dr. Emmeline Hill, who sent us a copy of her study and took the time to answer questions, and to Mr. Bowling, who reviewed the essay below, who is likewise not responsible for any misinterpretations. -- Patricia Erigero

Who's Your Momma? New Genetic Research and Old Pedigrees

Researchers at the prestigious Department of Genetics at Trinity College, Ireland, have uncovered probable deep-seated pedigree errors in the General Stud Book, as well as some more modern inaccuracies that affect the pedigrees of virtually all horses recorded in that book today. Since every other stud book in the world is based on the GSB, the findings apply to those authorities as well.

The study is the first to apply the power of genetic research to the specific histories of the most comprehensively documented domesticated animal in the world --
the Thoroughbred--where pedigree is one of the principal factors in the multibillion dollar worldwide business of breeding and selling racehorses.

The international team of genetic researchers, led by Dr. Emmeline Hill, published their findings, entitled "History and Integrity of Thoroughbred Dam Lines Revealed in Equine mtDNA Variation," in the August 2002 issue of Animal Genetics. Mitochrondrial DNA (mtDNA), present in every cell of every animal's body, is inherited solely from the mother, which allows tracing of a direct genetic line in maternal descent. MtDNA studies have revolutionized such diverse areas of study as human evolution and migration, the relationship between and evolution of wolves and domestic dogs, and genetic diversity among forest trees. The stability--and reliability--of maternal genetic inheritance in horses has been documented in previous studies of Lippizans and Arabians. The Trinity College study examined mitochrondrial DNA fragments from each horse in the sample population, using two methods of analysis, and then compared the results with historic records, beginning with the GSB.

Unlike chromosomal genes, mitochondrial DNA is transmitted as a unit, and its interpretation does not rely on probability statistics and other assessments to determine its reliability. In comparing mtDNA samples, they either match, or they do not. By combining the mtDNA research with the recorded pedigrees of the 100 horses sampled, researchers found a number of anomalies, some rooted at least as far back as the 17th century, and some discrepancies of more recent origin, dating back no further than the mid-19th century, and possibly even more recent. The reported results will require a reconsideration of pedigree interpretation based on historic dam lines that have largely lain unquestioned in the GSB since it was first published in 1791, over one hundred years after the earliest identified founding mares lived and produced foals.

The research confirms what some Thoroughbred historians have suspected--and in some cases proven--for decades: that the GSB got some of its pedigrees wrong, and that pedigree errors in maternal lines have persisted up to modern times. Because the GSB has been a closed registry, with minor modifications in its 200-plus year history, and sons and daughters of maternal lines have interbred many times, the study implies that the pedigree of virtually every Thoroughbred today is incorrect in one or more branches of its family tree, although not necessarily the direct female line.

Historic Organization of Female Lines

The study analyzed and mapped the mtDNA of 100 Thoroughbreds, located at facilities in Ireland, the U.S., and Australia. The results were compared with each horse's pedigree and line of female descent, as provided by the GSB.

These female lines were organized by the late 19th century researcher Bruce Lowe into numbered lines of maternal families, with the lowest numbers assigned to female lines with the most winners of certain English classic races up to that time. Lowe's work identified about 50 founding mares in the GSB, a number later augmented to 74 by other researchers. Bruce Lowe family numbers are widely used today as a means to easily identify thoroughbreds of related female descent.

The genetic sequences of the 100 horses sampled had pedigrees placing them within 19 of the families defined by Bruce Lowe: Family numbers 1 through 14, and family numbers 16, 17, 19, 22, and 25. The number of families (19), and number of horses in each family analyzed in the study were based on the population available for analysis, and so was not a random study. In its broadest terms, the study results indicate there were fewer than nineteen foundation mares in the nineteen families studied. Further, seven of the "families" actually trace to more than one founding mare; some branches belong to other families and some to mares yet to be identified.

One principal discovery in the study demonstrated that Thoroughbred foundation mares share mtDNA haplotypes (variants) far more than has been observed in other horse populations. Researchers determined that a number of Thoroughbred maternal lines or families, formerly thought to spring from unrelated mares, have common female founders, and that Thoroughbreds have a much higher frequency of "sharing" female lines than do other breeds that have been studied. Thoroughbreds, as historians of the breed have said for decades, spring from a small number of original mares, probably even fewer than previously thought.

The study identified only seventeen variants in the nineteen family lines studied; since two of the variants were due to a single difference, or de novo mutation, in the DNA sequence, it is probable the number of unique haplotypes, indicating different founding mares, is actually fifteen, within the nineteen families.

Because mtDNA does not vary over long periods of time -- the rate of mutation suggests 10,000 years or more -- the variants found in the Hill study can also be found in horse breeds from Europe, the Far East, and Near East. The Animal Geneticsarticle includes a chart, which shows a phylogenetic tree mapping the mtDNA haplotypes geographically, to which readers are referred. The genetic discoveries of the Hill study, then, must be interpreted within the framework of recorded history -- pedigrees and other historical records -- to examine the impact on the thoroughbred.